Running

Deep squats. Seriously, it builds up the muscles that support and protect the knee. Can have the side effect of squatters bum, where you develop muscles in your arse that you didn't know you had. That and the quads you develop from mixing cycling and squatting can make finding trousers that fit a challenge.

Edit: oh, just to be clear, this is barbell squats, not silly bodyweight squats.

The current trend of chinos is proving expensive.... getting sick of walking round with my dingles dangling out as well....

Single leg body weight squats can be effective as well if weights aren't your thing, or wearing a heavy backpack whilst doing them if you're bodyweight doesn't add up to much... But you're best with a barbell.